CT angiography (CTA) and MRI are non-invasive imaging modalities to assess coronary endothelial function (CEF). However, the performance of these techniques has yet to be quantitatively compared. Images of an in vitro phantom that simulates a physiological range of coronary artery cross-sectional areas (CSAs) were acquired using both CTA and MRI. CSAs were automatically measured and compared to the known nominal values. Statistical analysis suggests that MRI is capable of detecting significantly smaller CSA differences than CTA (2.25±0.80% vs. 7.42±0.63% for a 3-mm baseline diameter; p<0.0001), which is well within the range of physiological vasomotor responses of proximal coronary arteries.